HEADER VIRAL PROTEIN 22-MAR-22 7XC3 TITLE CRYSTAL STRUCTURE OF SARS-COV-2 NSP3 MACRODOMAIN 3 (SARS-UNIQUE TITLE 2 DOMAIN-M) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PAPAIN-LIKE PROTEASE NSP3; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NON-STRUCTURAL PROTEIN 3,NSP3,PL2-PRO,PAPAIN-LIKE COMPND 5 PROTEINASE,PL-PRO; COMPND 6 EC: 3.4.19.12,3.4.22.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_TAXID: 2697049; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA KEYWDS G-QUADRUPLEX-BINDING MACRODOMAIN, SARS-UNIQUE DOMAIN, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.LI,J.GAO REVDAT 3 29-NOV-23 7XC3 1 REMARK REVDAT 2 07-DEC-22 7XC3 1 JRNL REVDAT 1 23-NOV-22 7XC3 0 JRNL AUTH J.LI,F.ZHONG,M.LI,Y.LIU,L.WANG,M.LIU,F.LI,J.ZHANG,J.WU, JRNL AUTH 2 Y.SHI,Z.ZHANG,X.TU,K.RUAN,J.GAO JRNL TITL TWO BINDING SITES OF SARS-COV-2 MACRODOMAIN 3 PROBED BY JRNL TITL 2 OXAPROZIN AND MECLOMEN. JRNL REF J.MED.CHEM. V. 65 15227 2022 JRNL REFN ISSN 0022-2623 JRNL PMID 36356292 JRNL DOI 10.1021/ACS.JMEDCHEM.2C01168 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19_4092 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 36862 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.430 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 56.9900 - 4.1000 0.99 2791 160 0.1715 0.1799 REMARK 3 2 4.1000 - 3.2500 0.98 2584 149 0.1806 0.1869 REMARK 3 3 3.2500 - 2.8400 1.00 2594 148 0.2069 0.2352 REMARK 3 4 2.8400 - 2.5800 0.98 2524 145 0.2125 0.2394 REMARK 3 5 2.5800 - 2.4000 1.00 2541 145 0.2139 0.2319 REMARK 3 6 2.4000 - 2.2500 0.99 2547 147 0.1971 0.2316 REMARK 3 7 2.2500 - 2.1400 0.88 2232 128 0.1894 0.2232 REMARK 3 8 2.1400 - 2.0500 0.86 2206 126 0.1934 0.2145 REMARK 3 9 2.0500 - 1.9700 0.99 2492 143 0.2026 0.2256 REMARK 3 10 1.9700 - 1.9000 0.99 2491 143 0.2046 0.2585 REMARK 3 11 1.9000 - 1.8400 0.99 2475 143 0.2118 0.2291 REMARK 3 12 1.8400 - 1.7900 0.98 2474 142 0.2145 0.2658 REMARK 3 13 1.7900 - 1.7400 0.98 2462 141 0.2262 0.2752 REMARK 3 14 1.7400 - 1.7000 0.98 2449 140 0.2393 0.2563 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.480 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7XC3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1300028502. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36862 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 56.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.15400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.84800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 12.00 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2W2G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.5 M SODIUM FORMATE, PH 6.8, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 92.17100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 29.96200 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 29.96200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 46.08550 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 29.96200 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 29.96200 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 138.25650 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 29.96200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.96200 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 46.08550 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 29.96200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.96200 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 138.25650 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 92.17100 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 610 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 VAL A 635 -50.74 65.30 REMARK 500 TYR B 600 103.48 -160.03 REMARK 500 VAL B 635 -54.62 71.12 REMARK 500 REMARK 500 REMARK: NULL DBREF 7XC3 A 551 673 UNP P0DTC1 R1A_SARS2 1369 1491 DBREF 7XC3 B 551 673 UNP P0DTC1 R1A_SARS2 1369 1491 SEQADV 7XC3 PHE A 547 UNP P0DTC1 EXPRESSION TAG SEQADV 7XC3 GLN A 548 UNP P0DTC1 EXPRESSION TAG SEQADV 7XC3 HIS A 549 UNP P0DTC1 EXPRESSION TAG SEQADV 7XC3 MET A 550 UNP P0DTC1 EXPRESSION TAG SEQADV 7XC3 PHE B 547 UNP P0DTC1 EXPRESSION TAG SEQADV 7XC3 GLN B 548 UNP P0DTC1 EXPRESSION TAG SEQADV 7XC3 HIS B 549 UNP P0DTC1 EXPRESSION TAG SEQADV 7XC3 MET B 550 UNP P0DTC1 EXPRESSION TAG SEQRES 1 A 127 PHE GLN HIS MET GLY THR VAL SER TRP ASN LEU ARG GLU SEQRES 2 A 127 MET LEU ALA HIS ALA GLU GLU THR ARG LYS LEU MET PRO SEQRES 3 A 127 VAL CYS VAL GLU THR LYS ALA ILE VAL SER THR ILE GLN SEQRES 4 A 127 ARG LYS TYR LYS GLY ILE LYS ILE GLN GLU GLY VAL VAL SEQRES 5 A 127 ASP TYR GLY ALA ARG PHE TYR PHE TYR THR SER LYS THR SEQRES 6 A 127 THR VAL ALA SER LEU ILE ASN THR LEU ASN ASP LEU ASN SEQRES 7 A 127 GLU THR LEU VAL THR MET PRO LEU GLY TYR VAL THR HIS SEQRES 8 A 127 GLY LEU ASN LEU GLU GLU ALA ALA ARG TYR MET ARG SER SEQRES 9 A 127 LEU LYS VAL PRO ALA THR VAL SER VAL SER SER PRO ASP SEQRES 10 A 127 ALA VAL THR ALA TYR ASN GLY TYR LEU THR SEQRES 1 B 127 PHE GLN HIS MET GLY THR VAL SER TRP ASN LEU ARG GLU SEQRES 2 B 127 MET LEU ALA HIS ALA GLU GLU THR ARG LYS LEU MET PRO SEQRES 3 B 127 VAL CYS VAL GLU THR LYS ALA ILE VAL SER THR ILE GLN SEQRES 4 B 127 ARG LYS TYR LYS GLY ILE LYS ILE GLN GLU GLY VAL VAL SEQRES 5 B 127 ASP TYR GLY ALA ARG PHE TYR PHE TYR THR SER LYS THR SEQRES 6 B 127 THR VAL ALA SER LEU ILE ASN THR LEU ASN ASP LEU ASN SEQRES 7 B 127 GLU THR LEU VAL THR MET PRO LEU GLY TYR VAL THR HIS SEQRES 8 B 127 GLY LEU ASN LEU GLU GLU ALA ALA ARG TYR MET ARG SER SEQRES 9 B 127 LEU LYS VAL PRO ALA THR VAL SER VAL SER SER PRO ASP SEQRES 10 B 127 ALA VAL THR ALA TYR ASN GLY TYR LEU THR FORMUL 3 HOH *214(H2 O) HELIX 1 AA1 ASN A 556 ARG A 568 1 13 HELIX 2 AA2 THR A 577 TYR A 588 1 12 HELIX 3 AA3 THR A 612 ASN A 624 1 13 HELIX 4 AA4 ASN A 640 ARG A 649 1 10 HELIX 5 AA5 SER A 661 THR A 673 1 13 HELIX 6 AA6 ASN B 556 ARG B 568 1 13 HELIX 7 AA7 THR B 577 TYR B 588 1 12 HELIX 8 AA8 THR B 612 ASN B 624 1 13 HELIX 9 AA9 ASN B 640 ARG B 649 1 10 HELIX 10 AB1 SER B 661 THR B 673 1 13 SHEET 1 AA1 3 MET A 550 VAL A 553 0 SHEET 2 AA1 3 ALA A 655 SER A 658 1 O VAL A 657 N GLY A 551 SHEET 3 AA1 3 LEU A 627 THR A 629 1 N THR A 629 O SER A 658 SHEET 1 AA2 3 LEU A 570 CYS A 574 0 SHEET 2 AA2 3 ARG A 603 TYR A 607 1 O TYR A 605 N VAL A 573 SHEET 3 AA2 3 GLY A 596 ASP A 599 -1 N VAL A 598 O PHE A 604 SHEET 1 AA3 3 MET B 550 VAL B 553 0 SHEET 2 AA3 3 ALA B 655 SER B 658 1 O VAL B 657 N VAL B 553 SHEET 3 AA3 3 LEU B 627 THR B 629 1 N THR B 629 O THR B 656 SHEET 1 AA4 3 MET B 571 CYS B 574 0 SHEET 2 AA4 3 ARG B 603 TYR B 607 1 O ARG B 603 N MET B 571 SHEET 3 AA4 3 GLY B 596 ASP B 599 -1 N VAL B 598 O PHE B 604 CRYST1 59.924 59.924 184.342 90.00 90.00 90.00 P 41 21 2 16 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016688 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016688 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005425 0.00000